*UPDATE* If you update the CB config and servers ETPro you should be able to play no problem!

Ok well I've experienced a similar problem to many other people theres a few ways this could be problematic for you so here are a few issues and possible solutions:

The easiest way to get playing may be deleting the corresponding etpro archive and downloading the pk3 from the server again, this depends on the server setup, but it should work if your game is setup 'nicely'.

I'm a server admin I put the new config on but players get kicked by the md5 checks???
There's two issues here, if you're using the 3.2.3 version of etpro then players may need to extract these files in their etpro directory from the 3.2.3 etpro .pk3 file then they should be able to play.

If you put on the config but the server isnt on 3.2.3 then you need to either update the server or kill the md5 checks by manually entering: rcon "pb_sv_md5toolempty" (you dont have to be on the server)
This will remove all md5 checks but will be useless if you reload the config or load another map with the config active (I believe)

If you want to play with the latest config but you are having these problems open the .config files and head to line number 158, comment out the lines up to 162 which should look like this, your config will not be certified for wars but at least you'll be able to play!

I got onto a 3.2.x server but got kicked for md5 checks on cgame or mp_ui files?

You need to extract the files for the version of server you want to connect to, first find your game dir (yellow box) and go to etpro folder, then pick the .pk3 for the version you need to get working (blue box)
image: etproa

Open it with an archive program that can handle .zip files (winzip, winrar, 7zip..)
then extract the following files to your etpro dir (pink box)
image: etpro

I updated the server + configs, but I rolled them back, it's still happening?
Kill the md5 checks by manually entering: rcon "pb_sv_md5toolempty" (you dont have to be on the server)